Open source and DIY hardware for DNA nanotechnology labs

Setting up or upgrading a lab to conduct state-of-the-art DNA nanotechnology is not an inexpensive undertaking. The hardware alone can easily set you back several hundreds of thousands of dollars.

Analogous to the open-source software approach (think Linux or Apache), increasingly instruments and specialized equipment designs are also developed as part of a growing open source scientific hardware (OSSH) movement. Previously, we have already reported on how a group of nanotechnology students built a low cost (less than $500) Atomic Force Microscope using LEGO, or a cheap, homemade benchtop photolithography system for less than $30. Adding to the list, a recent article in the Journal of Biological Methods (“Open source and DIY hardware for DNA nanotechnology labs”) presents three examples of open source/do-it-yourself (DIY) technology with significantly reduced costs relative to commercial equipment.

“There are many reasons for exploring an open source approach to laboratory equipment,” says Peter B. Allen, an Assistant Professor at the University of Idaho, and senior author of the paper. “Open source equipment is more flexible and usually less expensive than the equivalent commercially produced experimental apparatus. While cost savings is an important consideration in and of itself, it also allows for researchers to take a smaller risk in trying a new procedure or exploring a new research interest. “A gel scanner design for scanning electrophoretically separated DNA” Here, an inexpensive ($100) office scanner was converted to fluorescence detection, achieving comparable sensitivity to a commercial instrument.

Although the original scanner itself is commercial, the researchers in their paper present the source code for the conversion with step-by-step instructions and a detailed list of materials required. In summary: green and red illumination sources were disabled. Green or red light would pass through the filter and cause unacceptable levels of background live reflected light. The blue light emitted by the scanner was preserved so that the scanner would pass its internal self-checks. A yellow wratten filter is then taped to the underside of the scanner bed. Side-on blue illumination (rather than the scanner’s internal blue LED) was then added for efficient exultation to increase the signal-to-noise.

A gel mold for horizontal polyacrylamide gel electrophoresis (PAGE) Polyacrylamide gel electrophoresis (PAGE) analysis and purification of DNA oligonucleotides is a prerequisite for many applications of DNA. DNA nanotechnology is usually built on the basis of smaller DNA fragments (under 100 bases). This requires the use of PAGE. The authors write that, with the advent of 3D printing, a gel casting form can be easily manufactured that allows for the polymerization of an acrylamide gel in the exact format necessary for horizontal gel rigs. Other techniques for creating gels appropriate for horizontal PAGE have been published. But this one has the distinction of using an open source, 3D printed gel mold which can be ordered or modified as needed.

A design for a homogenizer which can be attached to any reciprocating motor. This homogenizer can be used to generate colloidal particles from polyacrylamide which can be useful for multiple DNA-based applications including affinity chromatography, NexGen sequencing, or sample enrichment. This is considerably more customizable and less expensive than commercial sources of DNA-coated particles. Both designs can be downloaded, modified, and 3D printed in-house or ordered from a prototype manufacturer.

The cost savings of building rather than buying a piece of equipment can range from 50 to 90%. For the three examples described above, the savings are about 90% in each case. In the case of the scanner (cost ∼$200), it replaces a gel document system that costs several thousand dollars (greater than $2,000, used). In the case of the horizontal gel casting mold (cost ∼$30), it replaces a second gel rig that costs several hundred dollars (typical cost ∼$500-$1000 depending on size). In the case of the homogenizer (cost ∼$200 including motor and speed controller), it replaces a commercial tissue homogenizer that costs several thousand dollars (>$5000).

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